1. Sort the Proteins table by selecting the Sum PEP Score column.
  2. NOTE

    The human proteins are still filtered out in this list from the steps in Use the display filter to view E. coli proteins.

  3. Select the protein Elongation factor Tu 2 in the fourth row.
  4. Select Show Associated Tables at the bottom of the window.
  5. Select the Peptide Groups tab if it is not already selected in the Associated Table.
  6. Select View > Chromatogram Traces View to view the chromatograms for the selected peptide.
  7. NOTE

    The chromatograms are color-coded by their study factor by default. You can change this in the Group By checkboxes on the left side of the Chromatogram Traces view.

    When you select the study factor, the three replicates of each sample appear in the same color. As you can see by the plot, the chromatograms for the 15 ng sample are more abundant than the 10 ng, which is again more abundant than the 7.5 and 3 ng samples. This shows that the quantification results match the expectation for an E. coli peptide.

  8. Sort the Peptide Groups table alphabetically by selecting the Annotated Sequence column.
  9. Select the second peptide in the Peptide Groups list [K].FESEVYILSK.[D].
  10. The chromatogram traces view updates with the chromatograms for that specific peptide.
  11. The chromatographic peaks for this peptide are well aligned.
  12. The vertical lines on the plot show when that peptide was triggered for MS/MS during acquisition for that file.
  13. Also, triangles are shown at the apex of each chromatogram. The Precursor Ions Quantifier node allows changing the setting for peptide quantification between the apex intensity indicated by that triangle or the peak area indicated by the area shaded under the chromatogram.
  14. To see the effect of the retention time alignment, right-click the Chromatogram Traces View, select Display Options, and then select Show Unaligned.
  15. By default, the chromatograms display the results post retention time alignment.